Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate 209474 DVU0535 40.1 kd protein in hmc operon (HmcB)
Query= uniprot:A0A2R4BLY8 (215 letters) >MicrobesOnline__882:209474 Length = 370 Score = 92.0 bits (227), Expect = 1e-23 Identities = 72/229 (31%), Positives = 95/229 (41%), Gaps = 52/229 (22%) Query: 4 YAMVADLRRCVGCQTCTAACKHTNATP-PGVQWRWVLDVE------AGEFPDVSR----- 51 Y ++ D RC+GC+ C AC N P P ++ + +E A + V+R Sbjct: 40 YGVLHDTTRCIGCRKCEQACNEVNKLPAPKAKFDDLTVLEKTRRTDADSWTVVNRYNAAG 99 Query: 52 ----TFVPVGCQHCDEPPCETVCPTTATKKRADGLVTIDYDLCIGCAYCSVACPYNARYK 107 F C HC EP C + C A K DG VT D LC+GC YC VACP+N Sbjct: 100 LDHPVFRKQQCNHCLEPACASACFVKAFTKNPDGSVTYDGSLCVGCRYCMVACPFNV--- 156 Query: 108 VNFAEPAYGDRLMANEKQRADPARVGVATKCTFCSDRIDYGVAHGLTPGVDPDATPACAN 167 PA+ + DP + KCT C R+ A G PG C Sbjct: 157 -----PAF------QYAEAFDP----LIQKCTMCHPRL----AEGKLPG--------CVE 189 Query: 168 ACIANALTFGDIDDPNSKASRLLREN-----EHFRMHEELGTGPGFFYL 211 C ALTFG D A +R+N +H +E+G G + YL Sbjct: 190 ICPKEALTFGRRKDLVRIAHDRIRQNPGRYIDHVYGEQEMG-GTAWMYL 237 Lambda K H 0.323 0.137 0.461 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 282 Number of extensions: 21 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 215 Length of database: 370 Length adjustment: 26 Effective length of query: 189 Effective length of database: 344 Effective search space: 65016 Effective search space used: 65016 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory